A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-02-04, 23:29 CET
based on data in:
/data/medugorac/Shared/Maulik/projects/scalePopgen/work/69/91fb9daae2e407b8b4c1bbfd0c561a
summary statistics
summary statistics of individual sample and population.
Population-wise distribution of minor allele frequency
Distribution of mean minor allele frequency in a user-defined window
Sample-wise summary statistics of SNP counts
The SNP counts are calculated using plink2
Population-wise distribution of Expected heterozygosity
Distribution of expected heterozygosity in a user-defined window
Population-wise distribution of observed heterozygosity
Distribution of observed heterozygosity in a user-defined window
Genetic structure
analysis carried out to explore genetic structure of populations.
Fst-distance based NJ tree
Fst distances were calculated using plink and NJ distances were calculated using Biopython module
Principal Component Analysis (PCA)
PCA was carried out using smartpca program of eigensoft package
Q-matrices of ADMIXTURE analysis
Note that the color-pattern is not consistent across the different values of K
Identical by state (IBS) distance based Neighbor Joining (NJ) tree
1-IBS distance was calculated using plink and NJ distances were calculated using Biopyton module
cross-validation (CV) plot for ADMIXTURE analysis
Note that the color-pattern is not consistent across the different values of K
Treemix_p
Treemix_results.